Structure Characterization of Pseudouridine Kinase PsuK.

Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (ΨMP) and further hydrolyzing 5'-ΨMP to produce uracil and ribose 5'-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in . Here, we solved the crystal structures of apo-PsuK and its binary complex with Ψ or -methyl-pseudouridine (m1Ψ). The structure of PsuK showed a homodimer conformation assembled by its β-thumb region. PsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of PsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover.